@jbrowse/plugin-legacy-jbrowse 5.0.0-beta.7 → 5.0.0-beta.9

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Files changed (7) hide show
  1. package/esm/JBrowse1Connection/configSchema.d.ts +41 -25
  2. package/esm/JBrowse1Connection/model.d.ts +60 -37
  3. package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts +20 -22
  4. package/esm/NCListAdapter/NCListAdapter.d.ts +1 -1
  5. package/esm/NCListAdapter/NCListAdapter.js +4 -4
  6. package/esm/NCListAdapter/configSchema.d.ts +12 -18
  7. package/package.json +4 -4
package/esm/JBrowse1Connection/configSchema.d.ts CHANGED
@@ -17,35 +17,51 @@
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  * ```
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  */
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  declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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- /**
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- * #slot
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- */
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- readonly dataDirLocation: {
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- readonly type: "fileLocation";
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- readonly defaultValue: {
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- readonly uri: "https://mysite.com/jbrowse/data/";
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- readonly locationType: "UriLocation";
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- };
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- readonly description: "the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/";
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- };
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- /**
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- * #slot
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- */
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- readonly assemblyNames: {
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- readonly description: "name of the assembly the connection belongs to, should be a single entry";
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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+ assemblyNames: {
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ connectionId: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ dataDirLocation: {
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ name: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ type: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly name: {
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- readonly type: "string";
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- readonly defaultValue: "nameOfConnection";
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- readonly description: "a unique name for this connection";
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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  readonly assemblyNames: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "optional list of names of assemblies in this connection";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ type: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ connectionId: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  export default JBrowse1Connection;
package/esm/JBrowse1Connection/model.d.ts CHANGED
@@ -8,44 +8,76 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
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  configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly name: {
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- readonly type: "string";
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- readonly defaultValue: "nameOfConnection";
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- readonly description: "a unique name for this connection";
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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  readonly assemblyNames: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "optional list of names of assemblies in this connection";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
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+ type: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ connectionId: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>;
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  silent: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  }, "configuration" | "type"> & {
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  configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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- readonly dataDirLocation: {
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- readonly type: "fileLocation";
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- readonly defaultValue: {
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- readonly uri: "https://mysite.com/jbrowse/data/";
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- readonly locationType: "UriLocation";
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- };
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- readonly description: "the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/";
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+ assemblyNames: {
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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- readonly assemblyNames: {
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- readonly description: "name of the assembly the connection belongs to, should be a single entry";
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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+ connectionId: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ dataDirLocation: {
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ name: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ type: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly name: {
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- readonly type: "string";
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- readonly defaultValue: "nameOfConnection";
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- readonly description: "a unique name for this connection";
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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  readonly assemblyNames: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "optional list of names of assemblies in this connection";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ type: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ connectionId: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>;
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  type: import("@jbrowse/mobx-state-tree").ILiteralType<"JBrowse1Connection">;
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  }, {
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  loading: boolean;
@@ -57,18 +89,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  setLoading(loading: boolean): void;
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  } & {
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  afterAttach(): void;
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- addTrackConf(trackConf: Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
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- setSubschema(slotName: string, data: Record<string, unknown>): any;
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- setSlot(slotName: string, value: unknown): void;
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
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- addTrackConfs(trackConfs: (Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
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- setSubschema(slotName: string, data: Record<string, unknown>): any;
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- setSlot(slotName: string, value: unknown): void;
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
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- setTrackConfs(trackConfs: (Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
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- setSubschema(slotName: string, data: Record<string, unknown>): any;
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- setSlot(slotName: string, value: unknown): void;
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
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+ addTrackConf(trackConf: Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel): any;
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+ addTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
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+ setTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
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  } & {
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  connect(): Promise<void>;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts CHANGED
@@ -18,32 +18,30 @@
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  * ```
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  */
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  declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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- /**
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- * #slot
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- */
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+ type: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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  readonly namesIndexLocation: {
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- readonly type: "fileLocation";
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- readonly defaultValue: {
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- readonly uri: "/volvox/names";
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- readonly locationType: "UriLocation";
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- };
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- readonly description: "the location of the JBrowse1 names index data directory";
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
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  };
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- /**
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- * #slot
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- */
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  readonly tracks: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "List of tracks covered by text search adapter";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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- /**
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- * #slot
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- */
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  readonly assemblyNames: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "List of assemblies covered by text search adapter";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ textSearchAdapterId: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  export default _default;
package/esm/NCListAdapter/NCListAdapter.d.ts CHANGED
@@ -14,7 +14,7 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
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  /**
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  * Fetch features for a certain region.
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  * @param region -
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- * @param opts - [stopToken] optional stopTokenling object for aborting the fetch
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+ * @param opts - [signal] optional signalling object for aborting the fetch
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  * @returns Observable of Feature objects in the region
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  */
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  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/esm/NCListAdapter/NCListAdapter.js CHANGED
@@ -1,7 +1,7 @@
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  import NCListStore from '@gmod/nclist';
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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+ import { checkAbortSignal } from '@jbrowse/core/util/aborting';
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  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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- import { checkStopToken } from '@jbrowse/core/util/stopToken';
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  import { RemoteFile } from 'generic-filehandle2';
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  import NCListFeature from './NCListFeature.js';
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  export default class NCListAdapter extends BaseFeatureDataAdapter {
@@ -23,14 +23,14 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
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  /**
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  * Fetch features for a certain region.
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  * @param region -
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- * @param opts - [stopToken] optional stopTokenling object for aborting the fetch
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+ * @param opts - [signal] optional signalling object for aborting the fetch
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  * @returns Observable of Feature objects in the region
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  */
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  getFeatures(region, opts = {}) {
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  return ObservableCreate(async (observer) => {
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- const { stopToken } = opts;
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+ const { signal } = opts;
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  for await (const feature of this.nclist.getFeatures(region)) {
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- checkStopToken(stopToken);
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+ checkAbortSignal(signal);
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  observer.next(this.wrapFeature(feature));
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  }
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  observer.complete();
package/esm/NCListAdapter/configSchema.d.ts CHANGED
@@ -16,26 +16,20 @@
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  * ```
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  */
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  declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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- /**
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- * #slot
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- * URL of a JBrowse 1 NCList `trackData.json`, with `{refseq}` standing in
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- * for the reference sequence name — the per-reference directory layout
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- * `flatfile-to-json.pl` and `biodb-to-json.pl` write.
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- */
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+ type: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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  readonly rootUrlTemplate: {
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- readonly type: "fileLocation";
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- readonly defaultValue: {
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- readonly uri: "/path/to/my/{refseq}/trackData.json";
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- readonly locationType: "UriLocation";
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- };
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
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  };
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- /**
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- * #slot
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- */
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  readonly refNames: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "List of refNames used by the NCList used for aliasing";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  export default NCListAdapter;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-legacy-jbrowse",
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- "version": "5.0.0-beta.7",
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+ "version": "5.0.0-beta.9",
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  "type": "module",
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  "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
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  "keywords": [
@@ -22,12 +22,12 @@
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  ],
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  "dependencies": {
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  "@gmod/nclist": "^3.0.14",
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- "@jbrowse/mobx-state-tree": "^6.5.1",
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+ "@jbrowse/mobx-state-tree": "^6.5.2",
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  "generic-filehandle2": "^2.4.0",
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  "mobx": "^7.0.3",
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  "rxjs": "^7.8.2",
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- "@jbrowse/add-track-core": "^5.0.0-beta.7",
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- "@jbrowse/core": "^5.0.0-beta.7"
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+ "@jbrowse/add-track-core": "^5.0.0-beta.9",
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+ "@jbrowse/core": "^5.0.0-beta.9"
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  },
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  "publishConfig": {
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  "access": "public"